Coronavirus (SARS-Cov-2) sequencing analysis
Last Updated: 05.03.2021 (v9.0.0)
NOTE: This version of CoSA has only been tested with pbaa v0.1.3 and might not be compatible with pbaa versions above it
Stable version of CoSA under PacBio's GitHub
Developing version of CoSA under Magdoll's GitHub
Join the COVID19 Google Group to stay up-to-date on bioinfx recommendations and CoSA changes!
01.10.2022 v8.5.4 Updated to use raw read counts for small indel (<50bp) variant call filtering by vcfcons and reduces min_qual of variants to 60.
09.17.2021 v8.5.3 switch to sum(DP4) for large deletions to mitigate depth issues around deletion breakpoints
07.23.2021 v8.5.2 add POC for multi-strain detection.
07.21.2021 v8.5.1 adjust depth for snps spanned by deletions.
05.03.2021 v9.0.0 release. trim_MIPs.py added.
02.26.2021 v8.5.0 release. cleaned up unnecessary directories.
02.23.2021 v8.4.0 release. pbaa2vcf.py format update fix.
02.22.2021 v8.3.0 release. VCFCons.py now handles ill-formatted variants in CLC output.
02.21.2021 v8.2.0 release. pbaa2vcf.py now can handle edge cases of empty variants.
02.20.2021 v8.1.0 release. VCFCons.py can handle edge case of complete empty consensus and deals with unusual overlapping variant calls.
02.20.2021 v8.0.0 release. Added .vcfcons.variants.csv to VCFCOns.py output.
02.19.2021 v7.3.0 release. VCFCons.py accepts the new pbaa VCF type that follows standard AD info. Minor fixes to pbaa->VCF scripts.
02.17.2021 v6.1.0 release. Fixed VCFCons.py dealing with multiple ALT and proper INS if REF is more than 1nt.
02.15.2021 v6.0.0 release. Adding consensusVariants.py and pbaa2vcf.py for pbaa support.
02.14.2021 v5.2.0 release. VCFCons.py important bug fix on propagating deletions into consensus fasta.
02.11.2021 v4.0.0 release. VCFCons.py added.
CoSA is a set of Python and R scripts for analyzing SARS-CoV-2 sequences from PacBio HiFi/CCS data.
To install, clone the repo and install:
$ git clone https://github.com/PacificBiosciences/CoSA.git
$ cd CoSA
$ python setup.py build
$ python setup.py install